bad summary. it prompted you to accept the certificate upon first use and then pinned it which is far different than what you are describing in terms of security implications.
This is about making bad things harder for unskilled users at the cost of raising the standard for service providers. If you can set up an email server, you can use easyrsa or step-ca or some manual openssl to create your own root CA. Or, register your self-signed email server as a trusted root CA.
Personally, I use easyrsa for my internal CA (with domain path constraints because I'm paranoid) and letsencrypt for my mail server, but I require VPN access to the user ports on the mail server.